[English] 日本語
Yorodumi- PDB-6ag5: Crystal structure of Ard1 N-terminal acetyltransferase E88H/H127E... -
+Open data
-Basic information
Entry | Database: PDB / ID: 6ag5 | ||||||
---|---|---|---|---|---|---|---|
Title | Crystal structure of Ard1 N-terminal acetyltransferase E88H/H127E mutant from Sulfolobus solfataricus | ||||||
Components | N-alpha-acetyltransferase | ||||||
Keywords | TRANSFERASE / Acetyltransferase | ||||||
Function / homology | Function and homology information N-terminal methionine Nalpha-acetyltransferase NatE / N-terminal amino-acid Nalpha-acetyltransferase NatA / peptide-glutamate-alpha-N-acetyltransferase activity / NatA complex / peptide-serine-alpha-N-acetyltransferase activity / peptide alpha-N-acetyltransferase activity / metal ion binding Similarity search - Function | ||||||
Biological species | Sulfolobus solfataricus P2 (archaea) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.32 Å | ||||||
Authors | Chang, Y.Y. / Hsu, C.H. | ||||||
Funding support | Taiwan, 1items
| ||||||
Citation | Journal: Chem.Commun.(Camb.) / Year: 2020 Title: Adaptation of thermophilic acetyltransferase to a water-mediated catalytic mechanism. Authors: Chang, Y.Y. / Hagawa, S. / Hsu, C.H. #1: Journal: SCI REP / Year: 2015 Title: Structural Basis for Substrate-specific Acetylation of Nalpha-acetyltransferase Ard1 from Sulfolobus solfataricus Authors: Chang, Y.Y. / Hsu, C.H. | ||||||
History |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 6ag5.cif.gz | 84.5 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb6ag5.ent.gz | 61.2 KB | Display | PDB format |
PDBx/mmJSON format | 6ag5.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6ag5_validation.pdf.gz | 720.9 KB | Display | wwPDB validaton report |
---|---|---|---|---|
Full document | 6ag5_full_validation.pdf.gz | 723.3 KB | Display | |
Data in XML | 6ag5_validation.xml.gz | 10.1 KB | Display | |
Data in CIF | 6ag5_validation.cif.gz | 13.1 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ag/6ag5 ftp://data.pdbj.org/pub/pdb/validation_reports/ag/6ag5 | HTTPS FTP |
-Related structure data
Related structure data | 6ag4C 4r3kS S: Starting model for refinement C: citing same article (ref.) |
---|---|
Similar structure data |
-Links
-Assembly
Deposited unit |
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
Unit cell |
|
-Components
#1: Protein | Mass: 20512.717 Da / Num. of mol.: 1 / Mutation: H88E, E127H Source method: isolated from a genetically manipulated source Source: (gene. exp.) Sulfolobus solfataricus P2 (archaea) / Strain: P2 / Gene: AsArd1 / Production host: Escherichia coli (E. coli) References: UniProt: Q980R9, N-terminal amino-acid Nalpha-acetyltransferase NatA, N-terminal methionine Nalpha-acetyltransferase NatE |
---|---|
#2: Chemical | ChemComp-ACO / |
#3: Chemical | ChemComp-CA / |
#4: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
---|
-Sample preparation
Crystal | Density Matthews: 2.1 Å3/Da / Density % sol: 37.12 % |
---|---|
Crystal grow | Temperature: 283 K / Method: vapor diffusion, sitting drop / pH: 7 / Details: 20% Tacsimate pH 7.0 |
-Data collection
Diffraction | Mean temperature: 77 K |
---|---|
Diffraction source | Source: SYNCHROTRON / Site: NSRRC / Beamline: BL13C1 / Wavelength: 0.9765 Å |
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: Dec 24, 2013 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9765 Å / Relative weight: 1 |
Reflection | Resolution: 2.32→30 Å / Num. obs: 7313 / % possible obs: 99.4 % / Redundancy: 6.3 % / Net I/σ(I): 10.69 |
Reflection shell | Resolution: 2.3→2.32 Å |
-Processing
Software |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 4R3K Resolution: 2.32→21.314 Å / SU ML: 0.26 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 24.13 / Stereochemistry target values: ML
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.32→21.314 Å
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement TLS group |
|